Pigments are "molecules that absorb specific wavelengths
(energies) of light and reflect all others."

Pigments are colored: the color we see is the net
effect of all the light reflecting back at us.

Now, what do I mean by absorb?

Electrons in molecules can exist at specific energy
levels. Normally they exist at the lowest possible energy level they can.
However, if enough energy comes along to boost them into the next level,
they can "absorb" that energy and occupy that higher level. This is what
pigments do. The light they absorb contains' just the right amount' of energy
necessary to push them into the next level. Any light that does not have
enough or has too much energy can not be absorbed and is reflected.

The electron in the higher energy level, however,
does not 'want' to stay there(i.e. it is unstable). It 'wants' to return
to its normal lower energy level. In order to do this it must get rid or
release the energy that has put it into the higher energy state to begin
with. This can happen several different ways:

1) The extra energy can be converted into molecular
motion and lost as heat.

2) Some of the extra energy can be lost as heat energy,
while the rest is lost as light. This re-emission of light energy is called
florescence.

3)The energy, but not the e- itself, can be passed
onto another molecule. This is called resonance.

4)The energy and the e- can be transferred to
another molecule.

Plant pigments usually utilize the last two of these
reactions to convert the sun's energy into their own. When chlorophyll is
isolated from the enzymes it is associated with, the second scenario can
be seen to happen.

What should be the ideal pigment for chloroplasts?

A collection of pigments that would absorb all light
and thus appear Black seems a logical choice... but in fact we know this
is not true.. plants except for some of the red algae appear green or brown,
not black. Why? a number of possible explanation occur...

IF plants had pigments that absorbed UV and x-rays
this would mean that so much energy could be absorbed in light areas that
electrons could be knocked off their orbitals and the molecule destroyed..

IF plants absorbed IR and radio waves, there would
not be enough energy for electron transfer, just enough to warm up the molecule

Pigments that absorb in the visible region gain just
enough energy to boost an electron to the next level...

However even in this region, not all visible wavelengths
are abosrbed..there is some speculation that in the early competitive wars
between photosynthetic bacteria [ and we mean early 3 BYA] , plants
specialized so that some would absorb in the red, others green or blue.
The survivors in the long run are the one with pigments that absorbed in
the red/blue reflecting green.... at least on land.

What are these Pigment involved in Photosythesis?:

Chlorophyll a:
This is the most abundant pigment in plants. Chlorophyll a absorbs light
with wavelengths of 430nm(blue)
and 662nm(red).
It reflects green light strongly so it appearsgreento us. It contains a hydrophobic (fat soluble)
phytol chain that allow it to be embedded in a lipid membrane. The rest
of the structure called a tetrapyrrolic ring rests outside of the membrane
. It is this part of the pigment that absorbs the energy from light. The
metal at the center of the structure, Mg, can have variable oxidation
states . This means that it can accept and donate e- readily depending
of the situation. Its flexible, which is very important to the function
of the molecule.

Chlorophyll b:
This molecule has a structure similar to that of chlorophyll a. It absorbs
light of 453nm and 642 nm maximally. It is not as abundant as chlorophyll
a, and probably evolved later. It helps increase the range of light a
plant can use for energy.

Carotenoids: This
is a class of accessory pigments that occur in all photosynthetic
organisms. They are completely hydrophobic (fat soluble) and exist in
lipid membranes. Carotenoids absorb light maximally between 460 nm and
550 nm and appear red, orange, or yellow to us.

The most important function of carotenoids seems
to be protecting the plant from free radicals formed from ultra violet or
other radiation. Free radicals are dangerous because they contain an extra
odd e- they don't really want to have. This means that they are constantly
trying to get rid of this extra electron. They do this by attacking whatever
bonds they can.

In animal systems it is speculated that:

Vitamin E + radical oxidized ---> radical +
Vitamin E oxidized

Vitamin E oxidized + carotenoids ----> Vit
E + carotenoids oxidized

Carotenoids oxidized + Vit C ---> carotenoids
+ Vit C oxidized

In animals, the Vit C can be flushed out of the system
since it is soluble in water which none of the other molecules are. Whether
this same series of transfers occurs in plants is unknown. In humans, taking
Vit E or betacarotenes in themselves is not protection against oxidants
unless there is a supply of Vit C to flush it out.. Smokes who maintain
low levels of C are not helped with increases of the other 2.

In plants, as the vacuole is a generally safe aqueous
repository, the oxidized C may end up here, whereas carotenoids could not
....

Xanthophylls are a fourth common class of pigments.
They are essentially oxidized Carotenoids and contain oxygen. They are
usually red and yellow and do not absorb energy as well as cartenoids.
They are also fat soluble.

Anthocyanins are a fifth class of pigments. These
pigments contain Cu and are stored in the vacuole of a plant because they
unlike the other fat soluble pigments are water soluble.

Note the structure of the phycocyanins we in the
red algae and BG's. How does it differ substantially from the above pigments?